Rebuild example page and link to example. Add also a link to the publication. Doc review: document edge collapse ignores simplices of higher dimension.

2 files changed, 23 insertions, 18 deletions

diff --git a/src/python/doc/examples.rst b/src/python/doc/examples.rst
index a42227e3..76e5d4c7 100644
--- a/src/python/doc/examples.rst
+++ b/src/python/doc/examples.rst
@@ -7,27 +7,30 @@ Examples
 
 .. only:: builder_html
 
-    * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>`
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
-    * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>`
     * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>`
-    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
-    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
-    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
     * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
-    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
-    * :download:`plot_simplex_tree_dim012.py <../example/plot_simplex_tree_dim012.py>`
-    * :download:`plot_rips_complex.py <../example/plot_rips_complex.py>`
-    * :download:`plot_alpha_complex.py <../example/plot_alpha_complex.py>`
-    * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>`
+    * :download:`coordinate_graph_induced_complex.py <../example/coordinate_graph_induced_complex.py>`
+    * :download:`diagram_vectorizations_distances_kernels.py <../example/diagram_vectorizations_distances_kernels.py>`
     * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
-    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`functional_graph_induced_complex.py <../example/functional_graph_induced_complex.py>`
+    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
+    * :download:`nerve_of_a_covering.py <../example/nerve_of_a_covering.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`plot_alpha_complex.py <../example/plot_alpha_complex.py>`
+    * :download:`plot_rips_complex.py <../example/plot_rips_complex.py>`
+    * :download:`plot_simplex_tree_dim012.py <../example/plot_simplex_tree_dim012.py>`
+    * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_correlation_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py>`
     * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_complex_edge_collapse_example.py <../example/rips_complex_edge_collapse_example.py>`
+    * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>`
     * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>`
     * :download:`sparse_rips_persistence_diagram.py <../example/sparse_rips_persistence_diagram.py>`
-    * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
-    * :download:`coordinate_graph_induced_complex.py <../example/coordinate_graph_induced_complex.py>`
-    * :download:`functional_graph_induced_complex.py <../example/functional_graph_induced_complex.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
     * :download:`voronoi_graph_induced_complex.py <../example/voronoi_graph_induced_complex.py>`
-    * :download:`nerve_of_a_covering.py <../example/nerve_of_a_covering.py>`
+    * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>`
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 9eee5e14..62f81d0b 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -583,10 +583,12 @@ cdef class SimplexTree:
         return (normal0, normals, infinite0, infinites)
 
     def collapse_edges(self, nb_iterations = 1):
-        """Assuming the simplex tree is a 1-skeleton graph, this function collapse edges and resets the simplex tree
-        from the remaining edges.
+        """Assuming the simplex tree is a 1-skeleton graph, this method collapse edges (simplices of higher dimension
+        are ignored) and resets the simplex tree from the remaining edges.
         A good candidate is to build a simplex tree on top of a :class:`~gudhi.RipsComplex` of dimension 1 before
-        collapsing edges.
+        collapsing edges
+        (cf. :download:`rips_complex_edge_collapse_example.py <../example/rips_complex_edge_collapse_example.py>`).
+        For implementation details, please refer to :cite:`edgecollapsesocg2020`.
 
         :param nb_iterations: The number of edge collapse iterations to perform. Default is 1.
         :type nb_iterations: int